drake_md_report


HYPOTHESES

We selected only peaks seen in >1 of the 4 replicates (i.e. n = 2 or 3 or 4)


setup

how many FTICR reps per treatment type?

so we select formulae seen in at least 2 reps per treatment type


van krevelens

domains, baseline

fticr domains

VK by replication

VK by replication

VK by treatment

VK diagrams by treatment

VK unique

VK unique

unique to each amendment, in each incubation type


peaks


relative abundances

STATS

PERMANOVA

PERMANOVA

overall

#> 
#> Call:
#> adonis(formula = relabund_wide %>% select(aliphatic:other) ~      (Amendments + Moisture + Wetting + Suction + Homogenization)^3,      data = relabund_wide) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                                     Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                           2   0.14469 0.07235   7.749 0.04743  0.001 ***
#> Moisture                             1   0.21659 0.21659  23.197 0.07100  0.001 ***
#> Wetting                              1   0.00949 0.00949   1.017 0.00311  0.359    
#> Suction                              1   0.38693 0.38693  41.442 0.12683  0.001 ***
#> Homogenization                       1   0.17509 0.17509  18.753 0.05739  0.001 ***
#> Amendments:Moisture                  2   0.04272 0.02136   2.288 0.01400  0.053 .  
#> Amendments:Wetting                   2   0.05755 0.02878   3.082 0.01887  0.017 *  
#> Amendments:Suction                   2   0.02770 0.01385   1.483 0.00908  0.186    
#> Amendments:Homogenization            2   0.13843 0.06921   7.413 0.04538  0.001 ***
#> Moisture:Wetting                     1   0.01834 0.01834   1.964 0.00601  0.163    
#> Moisture:Suction                     1   0.05744 0.05744   6.152 0.01883  0.004 ** 
#> Moisture:Homogenization              1   0.00569 0.00569   0.610 0.00187  0.586    
#> Wetting:Suction                      1   0.04324 0.04324   4.631 0.01417  0.015 *  
#> Wetting:Homogenization               1   0.05857 0.05857   6.273 0.01920  0.005 ** 
#> Suction:Homogenization               1   0.02398 0.02398   2.568 0.00786  0.073 .  
#> Amendments:Moisture:Wetting          2   0.08924 0.04462   4.779 0.02925  0.002 ** 
#> Amendments:Moisture:Suction          2   0.03256 0.01628   1.744 0.01067  0.140    
#> Amendments:Moisture:Homogenization   2   0.04431 0.02216   2.373 0.01452  0.061 .  
#> Amendments:Wetting:Suction           2   0.03546 0.01773   1.899 0.01162  0.097 .  
#> Amendments:Wetting:Homogenization    2   0.02015 0.01007   1.079 0.00660  0.370    
#> Amendments:Suction:Homogenization    2   0.08434 0.04217   4.517 0.02765  0.004 ** 
#> Moisture:Wetting:Suction             1   0.02053 0.02053   2.199 0.00673  0.123    
#> Moisture:Wetting:Homogenization      1   0.01006 0.01006   1.078 0.00330  0.329    
#> Moisture:Suction:Homogenization      1   0.02606 0.02606   2.791 0.00854  0.080 .  
#> Wetting:Suction:Homogenization       1   0.01174 0.01174   1.257 0.00385  0.284    
#> Residuals                          136   1.26979 0.00934         0.41623           
#> Total                              172   3.05069                 1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

PERMANOVA for treatments

1.5 kPa intact cores

#> 
#> Call:
#> adonis(formula = intact_1_5 %>% select(aliphatic:other) ~ Amendments *      Moisture * Wetting, data = intact_1_5) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.00598 0.002992  0.4876 0.01265  0.761    
#> Moisture                     1   0.07655 0.076546 12.4747 0.16179  0.001 ***
#> Wetting                      1   0.05513 0.055131  8.9847 0.11653  0.001 ***
#> Amendments:Moisture          2   0.02610 0.013050  2.1268 0.05517  0.077 .  
#> Amendments:Wetting           2   0.04201 0.021005  3.4232 0.08880  0.018 *  
#> Moisture:Wetting             1   0.01159 0.011590  1.8888 0.02450  0.136    
#> Amendments:Moisture:Wetting  2   0.05326 0.026629  4.3398 0.11257  0.006 ** 
#> Residuals                   33   0.20249 0.006136         0.42800           
#> Total                       44   0.47311                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

50 kPa intact cores

#> 
#> Call:
#> adonis(formula = intact_50 %>% select(aliphatic:other) ~ Amendments *      Moisture * Wetting, data = intact_50) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.08911 0.044557  5.8120 0.19613  0.001 ***
#> Moisture                     1   0.01105 0.011052  1.4416 0.02432  0.253    
#> Wetting                      1   0.01364 0.013645  1.7798 0.03003  0.175    
#> Amendments:Moisture          2   0.03580 0.017902  2.3352 0.07880  0.064 .  
#> Amendments:Wetting           2   0.02310 0.011549  1.5064 0.05084  0.225    
#> Moisture:Wetting             1   0.02864 0.028638  3.7355 0.06303  0.029 *  
#> Amendments:Moisture:Wetting  2   0.02301 0.011506  1.5008 0.05065  0.231    
#> Residuals                   30   0.22999 0.007666         0.50620           
#> Total                       41   0.45436                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

1.5 kPa homogenized cores

#> 
#> Call:
#> adonis(formula = homo_1_5 %>% select(aliphatic:other) ~ Amendments *      Moisture * Wetting, data = homo_1_5) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.11836 0.059179  7.8805 0.16732  0.001 ***
#> Moisture                     1   0.20554 0.205538 27.3701 0.29057  0.001 ***
#> Wetting                      1   0.01826 0.018258  2.4313 0.02581  0.077 .  
#> Amendments:Moisture          2   0.02901 0.014506  1.9317 0.04102  0.106    
#> Amendments:Wetting           2   0.04013 0.020065  2.6719 0.05673  0.046 *  
#> Moisture:Wetting             1   0.01276 0.012762  1.6995 0.01804  0.167    
#> Amendments:Moisture:Wetting  2   0.05051 0.025255  3.3630 0.07140  0.021 *  
#> Residuals                   31   0.23280 0.007510         0.32910           
#> Total                       42   0.70737                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

50 kPa homogenized cores

#> 
#> Call:
#> adonis(formula = homo_50 %>% select(aliphatic:other) ~ Amendments *      Moisture * Wetting, data = homo_50) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.19043 0.095213  6.6889 0.22699  0.001 ***
#> Moisture                     1   0.00609 0.006088  0.4277 0.00726  0.668    
#> Wetting                      1   0.03251 0.032511  2.2839 0.03875  0.128    
#> Amendments:Moisture          2   0.07283 0.036415  2.5582 0.08681  0.046 *  
#> Amendments:Wetting           2   0.03047 0.015235  1.0703 0.03632  0.407    
#> Moisture:Wetting             1   0.00969 0.009687  0.6805 0.01155  0.524    
#> Amendments:Moisture:Wetting  2   0.05565 0.027826  1.9548 0.06634  0.101    
#> Residuals                   31   0.44127 0.014235         0.52599           
#> Total                       42   0.83893                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

PCA

overall PCA

PCA individual treatments

individual cores


others

other plots

NOSC

elements

Session Info

click to expand

Date run: 2020-08-10

#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.6
#> 
#> Matrix products: default
#> BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] patchwork_1.0.1  visNetwork_2.0.9 vegan_2.5-6      lattice_0.20-41  permute_0.9-5    rmarkdown_2.3   
#>  [7] drake_7.12.4     ggbiplot_0.55    PNWColors_0.1.0  forcats_0.5.0    stringr_1.4.0    dplyr_1.0.1     
#> [13] purrr_0.3.4      readr_1.3.1      tidyr_1.1.1      tibble_3.0.3     ggplot2_3.3.2    tidyverse_1.3.0 
#> [19] here_0.1        
#> 
#> loaded via a namespace (and not attached):
#>  [1] httr_1.4.2        jsonlite_1.7.0    splines_4.0.2     modelr_0.1.8      assertthat_0.2.1  base64url_1.4    
#>  [7] blob_1.2.1        cellranger_1.1.0  yaml_2.2.1        progress_1.2.2    pillar_1.4.6      backports_1.1.8  
#> [13] glue_1.4.1        digest_0.6.25     rvest_0.3.6       colorspace_1.4-1  htmltools_0.5.0   Matrix_1.2-18    
#> [19] plyr_1.8.6        pkgconfig_2.0.3   broom_0.7.0       haven_2.3.1       scales_1.1.1      mgcv_1.8-31      
#> [25] txtq_0.2.3        generics_0.0.2    farver_2.0.3      ellipsis_0.3.1    withr_2.2.0       cli_2.0.2        
#> [31] magrittr_1.5      crayon_1.3.4      readxl_1.3.1      evaluate_0.14     storr_1.2.1       fs_1.5.0         
#> [37] fansi_0.4.1       nlme_3.1-148      MASS_7.3-51.6     xml2_1.3.2        tools_4.0.2       prettyunits_1.1.1
#> [43] hms_0.5.3         lifecycle_0.2.0   munsell_0.5.0     reprex_0.3.0      cluster_2.1.0     compiler_4.0.2   
#> [49] rlang_0.4.7       grid_4.0.2        rstudioapi_0.11   htmlwidgets_1.5.1 igraph_1.2.5      labeling_0.3     
#> [55] gtable_0.3.0      DBI_1.1.0         R6_2.4.1          lubridate_1.7.9   knitr_1.29        utf8_1.1.4       
#> [61] filelock_1.0.2    rprojroot_1.3-2   stringi_1.4.6     parallel_4.0.2    Rcpp_1.0.5        vctrs_0.3.2      
#> [67] dbplyr_1.4.4      tidyselect_1.1.0  xfun_0.16